tbuckley/cabot-search huggingface dataset:
Abstract 148: New conformational details help in clarifying Raf activation by dimerization
Authors: Mingzhen Zhang, Ryan Maloney, Hyunbum Jang, Ruth Nussinov
Journal: Cancer Research (2022)

Abstract Raf is a family of serine/threonine kinases in the mitogen-activated protein kinase (MAPK) pathway for cell proliferation. The full activation of Raf requires the dimerization of the kinase domain. The dimer interface of Raf has been regarded as an important therapeutic target against cancer. The next generation paradox breakers target the Raf dimerization. Despite the clinical importance, it remains unclear that how the transverse side-to-side dimerization promotes the OFF-to-ON transition of Raf’s kinase domain, and how the activated ON-state kinase domain can be stabilized in the dimer for Raf signaling. In this work, we uncover an atomic-level mechanism of Raf activation through dimerization, addressing these questions. The mechanism shows that the replacement of the intramolecular π-π stacking by the intermolecular π-π stacking at the dimer interface promotes the Raf activation. It releases the structural constraint of the αC-helix, inducing a series of conformational changes for the OFF-to-ON transition, such as the disruption of the inhibitory hydrophobic interactions and the approach of phosphorylation sites in A-loop to HRD motif for cis-autophosphorylation. Once activated, the ON-state kinase domain can be stabilized by the N-terminal basic (NtB) motif in the dimer for Raf signaling. This work provides the high-resolution structural insights into the Raf activation, suggesting a new structural strategy for drug discovery against Raf dimerization. Funded by Frederick National Laboratory for Cancer Research, National Institutes of Health, under contract HHSN261201500003I. Citation Format: Mingzhen Zhang, Ryan Maloney, Hyunbum Jang, Ruth Nussinov. New conformational details help in clarifying Raf activation by dimerization [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 148.
Abstract 5890: The effect of healthy eating on breast cancer-specific outcomes: A systematic review and meta-analysis
Authors: Eric Han, Vanessa Kady, Kayla Montan, Marjona Normuminova, Soomin Eum, Michael Rovito, Eunkyung Lee
Journal: Cancer Research (2022)

Abstract Background: Breast cancer (BC) survivors attempt to change their diet after diagnosis to improve cancer-specific outcomes; however, there are many sets of guidelines available, and cancer survivors are not sure which ones are best to follow. Therefore, we examined the effect of different dietary quality indices on BC-specific outcomes in BC survivors. Methods: Web of Science and EBSCOhost were searched for relevant publications using the key terms in June 2021. Covidence software was then used for the screening and extraction of these publications. Characteristics for the included studies such as, participants, and dietary quality index were examined, and summary effect sizes were estimated for BC recurrence and BC-specific mortality using a random-effects model. Results: Across the 10 included studies (9 BC-specific mortality and 1 Recurrence; 8 Post-diagnosis and 3 pre-diagnosis diet studies), a total of 25,194 BC survivors were included in the meta-analysis, and 2,550 BC-specific deaths and 461 recurrences were observed over a follow up period of 6-17.2 years. The dietary indices evaluated were ACS (n=2), CHFP (n=2), MDS (n=2), DASH (n=3), HEI (n=8), DQIR (n=1), and RFS (n=1). Meta-analysis showed that adhering to dietary guidelines after diagnosis was associated a 4~36% reduction in BC-specific mortality with varying degrees of significance: ACS (HR=0.96, 95% CI=0.72-1.29), CHFP (HR=0.64, 95% CI=0.49-0.83), MDS (HR=0.93, 95% CI=0.70-1.24), DASH (HR=0.79, 95% CI=0.64-0.98), and HEI (HR=0.93, 95% CI=0.70-1.24). Subgroup analysis with DASH guidelines showed that the strength of the association was greater for those with ER-positive, PR-negative, or HER2-positive cancer, physically active, and older survivors compared to their respective counterparts. Only one study evaluated BC recurrence, which was insufficient to perform meta-analysis, and pre-diagnosis adherence to dietary guidelines was not associated with BC-specific mortality (HR=0.98, 95% CI=0.81-1.17). Conclusions: Healthcare providers may find it best to encourage BC survivors to comply with the DASH or CHFP dietary guidelines to improve cancer-specific mortality. Additional research should be performed to strengthen the relationship found between adherence to dietary indices and breast cancer-specific outcomes. Keywords: dietary guidelines, diet quality, breast cancer mortality, DASH, meta-analysis Citation Format: Eric Han, Vanessa Kady, Kayla Montan, Marjona Normuminova, Soomin Eum, Michael Rovito, Eunkyung Lee. The effect of healthy eating on breast cancer-specific outcomes: A systematic review and meta-analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5890.
Abstract LB529: Oncogenic KRas plays a significant role in regulating expression of IDO1
Authors: Eunji Lee, Felicia He, Byeong Hyeok Choi, Wei Dai
Journal: Cancer Research (2022)

Abstract Ras proteins are among the most widely studied proto-oncogene products. Ras proteins are membrane-anchored GTPases that participate in multiple signaling cascades regulating crucial cellular processes including cell survival, proliferation, and differentiation. Ras mutations and/or deregulated Ras activities frequently lead to inflammation and malignant transformation. Recent studies have also shown that Ras mutations are associated with immuno-resistance by positive regulation of PD-L1 expression. Indoleamine 2,3-dioxygenases 1 (IDO1) is a heme-containing enzyme that catalyzes the rate limiting step of conversion of tryptophan into kynurenine (Kyn). Extensive research in the past has shown that IDO1 and its catalytic product Kyn mediate immune tolerance, thus promoting tumorigenesis in vivo. IDO1 expression is activated by immune cytokines including interferon-γ (IFN-γ)and interleukin-6 (IL-6). However, whether there is a mechanistic link between oncogenic KRas and IDO1 expression and how IDO1 expression contributes to immune invasion of transformed cells with KRas mutations remain unclear. Here we report that oncogenic KRas significantly enhanced IFN-γ-induced IDO1 expression. In H358 lung carcinoma cells, IDO1 expression induced by IFN-γ was at least in part dependent on ERK activation, and treatment with ARS-1620, a covalent KRasG12C inhibitor, suppressed IDO1 expression induced by IFN-γ in a concentration-dependent manner. IDO1 expression was also induced by IFN-γ in HCT116 colon carcinoma cells that harbored a KRasG12D mutant allele, but not in HCT116 cells with wild-type KRas, suggesting that IFN-γ induced IDO1 expression requires Ras activation. In addition, KRas downregulation by specific siRNAs decreased IFN-γ-induced IDO1 expression in A549 lung cancer cells. Taken together, our study strongly suggests that Ras/ERK signaling pathway plays an important role in promoting IDO1 expression induced by IFN-γ. Citation Format: Eunji Lee, Felicia He, Byeong Hyeok Choi, Wei Dai. Oncogenic KRas plays a significant role in regulating expression of IDO1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB529.
Abstract 2408: Elevated phosphate promotes a pro-migration phenotype in lung cancer
Authors: Jamie Arnst, George Beck
Journal: Cancer Research (2022)

Abstract Despite advances in treatment, metastasis remains a major cause of cancer-associated death in the US. Thus, identification of intrinsic and extrinsic factors that promote or inhibit tumor migration and invasion are critical. Increasingly, the dysregulation of cellular metabolism is being linked not only to tumor growth but tumor cell migration. Phosphorus (Pi) is an essential micronutrient necessary for energy metabolism, cell signaling via ATP, formation of nucleic acids and the cell membrane, and mineralization of the skeleton. Unsurprisingly, high levels of Pi are observed in tumor tissue compared to normal tissue, consistent with a demand for this metabolite in rapidly growing cells. Further, our lab has reported that high extracellular Pi increases cell growth, alters gene expression and protein translation, and promotes angiogenesis. High dietary Pi levels has also been shown to increase tumorigenesis in both lung and skin cancer models. However, it remains unknown how phosphate metabolism affects tumor migration and invasion. Here we report that high levels of Pi increases gene expression of EMT-related genes such as Twist, Vimentin, CD44, and OPN in the lung cancer cell line, A549. Further, increased Pi promotes tumor cell migration in a transwell assay and decreased Pi levels or inhibition of phosphate transport by phosphonoformic acid (PFA) impaired migration. Suggesting that high Pi can promote a pro-migration phenotype by upregulating EMT in cancer cells and by increasing directed cell migration. Ongoing research will focus on how intracellular Pi flux changes during cell invasion using a novel FRET-based phosphate sensor in vitro and the effect of Pi inhibition on metastasis in vivo. These findings provide further evidence for the role dysregulated Pi metabolism in promoting cancer progression and the potential for therapeutic intervention with broad impacts on patient outcomes. Citation Format: Jamie Arnst, George Beck. Elevated phosphate promotes a pro-migration phenotype in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2408.
Abstract 3103: Liquid tumor orthotopic PDX models of acute leukemia
Authors: Hongkui Chen, Lintao Bi, Shizhu Zhao, Shuai Wang, Wenqiang Huang, Josh Caggiula, Loc Van, Danyi Wen
Journal: Cancer Research (2022)

Abstract Liquid tumor orthotopic xenograft models were established by intra femoral injection on NCG mice using freshly prepared leukemia cells from peripheral blood (PB) or bone marrow (BM) of AML/ALL patient samples. The establishment of the orthotopic models were monitored by the flow cytometry analysis of peripheral blood of engrafted mice:CD45+/CD33+ for AML and CD45+/CD19+ for B-ALL. The double positive cells in the peripheral blood of the successfully transplanted model can reach 5-15%. Typically, it takes 120 -170 days to establish the P0 AML orthotopic model. It takes 45-60 days to establish the P0 ALL orthotopic model. Spleen from engrafted P0 mice was used for P1-P3 reconstitution of the orthotopic model. On these orthotopic models, we tested whether medicines such as etoposide, cytarabine, vincristine, ibrutinib and imatinib are sensitive. And anti-CD47 antibody was also tested on these models. NGS profiling was used to confirm the genotype of established orthotopic PDX. Citation Format: Hongkui Chen, Lintao Bi, Shizhu Zhao, Shuai Wang, Wenqiang Huang, Josh Caggiula, Loc Van, Danyi Wen. Liquid tumor orthotopic PDX models of acute leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3103.
Abstract 2633: Discovery of novel, highly selective inhibitors of PLK4 that demonstrate <i>in vivo</i> regressions in TRIM37 high xenografts
Authors: Kyle A. Edgar, Amy Young, Jared Moore, Xi Chen, Wei Fang, Jae H. Chang, Wayne Kong, Jason E. Long, Aleksandr Pankov, Anneleen Daemen, Daniel G. Shore, Robert Warne, Paul Gibbons, Chudi O. Ndubaku, Melissa R. Junttila, Lori S. Friedman
Journal: Cancer Research (2022)

Abstract Amplification and copy number alterations of the 17q23 amplicon are common in breast cancer and neuroblastoma and have been associated with early relapse and poor prognosis. Recent work identified a key vulnerability associated with amplicon-driven overexpression of TRIM37 in these tumor types (Meitinger et al. 2020; Yeow et al. 2020). High levels of TRIM37 prevent acentrosomal spindle assembly and render cells mitotically vulnerable to inhibition of polo-like kinase 4 (PLK4), a serine/threonine protein kinase that controls centrosome duplication. We have discovered potent small molecule inhibitors of PLK4 that are highly selective against the kinome, including against the closely related aurora kinases and PLK1-3. Self-regulation of PLK4 protein levels occurs through proteasomal degradation induced by PLK4 trans-autophosphorylation. ORIC PLK4 inhibitors blocked trans-autophosphorylation leading to stabilization of PLK4, thus directly demonstrating target inhibition in cells. Importantly, PLK4 inhibitor induced PLK4 protein stabilization correlated with cell viability, providing a quantifiable pharmacodynamic (PD) association with antitumor activity. Cell viability assessment across a cancer cell line panel revealed that the highly selective ORIC PLK4 inhibitors showed greater potency in TRIM37 high cancer cell lines as compared to TRIM37 low cell lines. In contrast, less selective compounds, including from the clinical literature, did not display differential potency in TRIM37 high versus low cancer cell lines. Importantly, cell potency in TRIM37 high cancer cells was rescued with knockdown of TRIM37, illustrating that selective PLK4 inhibitors are synthetic lethal with TRIM37 amplification. Oral administration of ORIC PLK4 inhibitors resulted in regressions of TRIM37 high xenograft tumors, with corresponding PD effects and no body weight loss. In summary, we have discovered novel, potent, highly selective small molecule inhibitors of PLK4 that are orally bioavailable and confirmed the potential for this new target in treating tumors with high levels of TRIM37. Citation Format: Kyle A. Edgar, Amy Young, Jared Moore, Xi Chen, Wei Fang, Jae H. Chang, Wayne Kong, Jason E. Long, Aleksandr Pankov, Anneleen Daemen, Daniel G. Shore, Robert Warne, Paul Gibbons, Chudi O. Ndubaku, Melissa R. Junttila, Lori S. Friedman. Discovery of novel, highly selective inhibitors of PLK4 that demonstrate in vivo regressions in TRIM37 high xenografts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2633.
Abstract 5784: Overcoming FFPE hurdles to enable high quality hybrid capture libraries and somatic mutation detection in matched tumor-normal patient samples
Authors: Margaret R. Heider, Jian Sun, Brittany S. Sexton, Bradley W. Langhorst, Andrew Gray, Lauren Higgins, Lixin Chen, Lynne Apone, Thomas C. Evans, Nicole M. Nichols, Eileen T. Dimalanta, Theodore B. Davis, Pingfang Liu
Journal: Cancer Research (2022)

Abstract In cancer genomics, a common source of DNA is formalin-fixed, paraffin-embedded (FFPE) tissue from patient surgical samples, where in most cases high quality fresh or frozen tissue samples are not available. FFPE DNA poses many notable challenges for preparing NGS libraries, including low input amounts and highly variable damage from fixation, storage, and extraction methods. Due to the high cost of sequencing and variability of coverage, regions of interest are often specifically enriched using hybrid capture-based approaches, but these methods require a high input of diverse, uniform DNA library to achieve the coverage required for somatic mutation identification in tumor samples.We applied a multi-faceted approach to improving the yield, quality, and coverage from libraries generated from cancer patient sample sets. Using tumor-normal pairs, we evaluated the impact of our method on the sensitivity and accuracy of somatic variant detection. Matched frozen tissue provided a truth set of somatic variants for a particular tumor as well as a gold standard by which we could assess the quality of our FFPE hybrid capture libraries. Combining DNA damage repair and a novel enzymatic fragmentation mix upstream of library preparation not only reduced the false positive rate in somatic variant detection by repairing damage-derived mutations but also improved the library yield, complexity, coverage uniformity, and hybrid capture library quality metrics. The use of unique molecular identifier (UMI)-containing adaptors ensured accurate duplicate marking. Finally, a new PCR master mix boosts the library yield without compromising library quality in FFPE samples ranging from very poor quality to high quality. This combinatorial approach allows even the poorest quality FFPE samples to achieve high quality libraries with sufficient input for hybrid capture in our study. Citation Format: Margaret R. Heider, Jian Sun, Brittany S. Sexton, Bradley W. Langhorst, Andrew Gray, Lauren Higgins, Lixin Chen, Lynne Apone, Thomas C. Evans, Nicole M. Nichols, Eileen T. Dimalanta, Theodore B. Davis, Pingfang Liu. Overcoming FFPE hurdles to enable high quality hybrid capture libraries and somatic mutation detection in matched tumor-normal patient samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5784.
Abstract 6025: Baseline cytokine profiling in naïve and tumor-bearing Balb/c and C57BL/6 Charles River mice
Authors: Kenneth Munroe, Christoph S. Eberle, Robert Mihalek, Stephen Festin
Journal: Cancer Research (2022)

Abstract Background: Syngeneic studies are still the backbone of oncology research. These rely on immunocompetent mice to model anti-cancer immune responses elicited by experimental treatments. Cytokines mediate these responses through cell signaling, which contributes to an immunosuppressive milieu in the tumor microenvironment. Determining the secretion patterns of these protein modulators can help understand pathogenesis, disease progression and resistance to targeted therapies. To evaluate biological effects of potential interventions, we compared systemic cytokine activities in naïve and untreated tumor-bearing Balb/c and C57BL/6 mice. Study Details: Charles River wild type Balb/c (n=9) and C57BL/6 (n=10) mice were used for all experiments. CT26 and B16.F10 tumor cell lines for inoculations were purchased from ATCC (Manassas, VA). Serum samples were collected from colon carcinoma (Balb/c) and melanoma (C57BL/6) bearing mice as well as tumor-free animals. For rapid multiplex measurements on the Meso Scale Discovery platform the V-PLEX Proinflammatory Panel 1 Mouse Kit was used (cat no. K15048D-1). IFN-γ, IL-1β, IL-2, IL-4, IL-5, IL-6, KC/GRO, IL-10, IL-12p70, and TNF-α were detected simultaneously by electrochemiluminescence within the manufacturer’s specification for each analyte. Results: Sera from CT26 and B16.F10 tumor-bearing mice exhibited higher average concentrations of IFN-γ, IL1-β, IL-4, IL-10, KC/GRO and TNF-α, when compared to naïve mice of the Balb/c or C57BL/6 background, respectively; however, IL-2 production was found increased in tumor-bearing Balb/c and decreased in tumor-bearing C57BL/6 mice. Though known to be promoting tumor growth, IL-6 was only measurable in three out of ten B16.F10-bearing mice and below the limit of detection in CT26-bearing mice. IL-5 and IL-12 p70 levels showed no difference between CT26-bearing and naïve Balb/c mice, whereas both cytokines were elevated in the B16.F10 model over naïve C57BL/6 mice. Conclusions: Circulating serum cytokines have been quantified in commonly used syngeneic mouse strains with and without tumor burden. These reference data provide baseline levels to compare soluble proinflammatory biomarkers suitable for assessing potential immunomodulatory effects of experimental cancer treatments in combination with other pharmacodynamic readouts. Citation Format: Kenneth Munroe, Christoph S. Eberle, Robert Mihalek, Stephen Festin. Baseline cytokine profiling in naïve and tumor-bearing Balb/c and C57BL/6 Charles River mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6025.
Abstract 5082: Proteomic analysis of extracellular vesicles from oncology donor samples purified using an alternating current electrokinetic microelectrode chip
Authors: Juan P. Hinestrosa, Jean M. Lewis, David J. Searson, Heath I. Balcer, David J. Gonzalez, Rajaram Krishnan
Journal: Cancer Research (2022)

Abstract In this study, we evaluated the ability to detect novel proteins on extracellular vesicles (EVs) following isolation using an alternating current electrokinetic (ACE) microarray. EVs circulating in blood contain a wealth of biomarkers that are thought to reflect the tumor’s proteome; however, detecting the full diversity of EV proteins may depend on choice of method to purify EVs for analysis. We compared an ACE microarray isolation method with a conventional chemical precipitation method to isolate EVs from blood plasma cancer and control samples. EVs were isolated from 1 mL each of control or pancreatic cancer patient plasma using the ExoVerita platform (Biological Dynamics) or ExoQuick Ultra kit (System Biosciences). Purified EVs were processed using tandem mass tag (TMT)-based multiplexing mass spectrometry proteomics (ThermoFisher Scientific) and the resulting peptide spectra were analyzed and quantified to determine the proteins present. Additional analyses, such as bioanalyzer measurements of contaminating plasma proteins and nanoparticle tracking analysis were performed in parallel to further characterize the isolated EVs. Cancer EVs isolated by ACE were enriched in proteins related to cancer functions when compared to non-cancer control EVs. They also showed enrichment in ontology clusters such as NABA core matrisome proteins, with depressed expression of wound healing family proteins. In contrast, EVs isolated using chemical purification demonstrated enrichment chiefly in proteins functionally grouped into immune system or blood regulation functions. After analyzing EVs isolated by ACE, a total of fifty-one (51) proteins were observed to be upregulated in the cancer donor samples. EV isolation method choice significantly impacted the proteomic profile observed. EV isolation using ACE-based technology can provide more insights into understanding the proteome by possibly reducing or removing non-specific proteins from the EVs. With better separation of EVs from blood proteins, the EV proteins identified may have greater biological significance. Citation Format: Juan P. Hinestrosa, Jean M. Lewis, David J. Searson, Heath I. Balcer, David J. Gonzalez, Rajaram Krishnan. Proteomic analysis of extracellular vesicles from oncology donor samples purified using an alternating current electrokinetic microelectrode chip [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5082.